found not dataset

[knakamura6222053]

Hi Developer!

I add "options(buildtools.check = function(action) TRUE)" so that I successed install

However, snakemake does not work. I was told that I don't have the required data set.

Maybe, I think "snakemake -n Paper_figures/all_figures_R" ? , but this also gave the same error.

##############################################################################################
error message

FileNotFoundError in file /var/folders/7d/rr7nqs8x1wq5rv74p18z5ctr0000gn/T/tmp_w5d0ky_, line 575:
[Errno 2] No such file or directory: '/path/to/data/storage/fraser/fraser2/mito/processed_data/variants/prokisch_dna_ids.txt'
File "/Users/idrc/Desktop/FRASER-2.0-analysis-main/Snakefile", line 6, in
File "/Users/idrc/anaconda3/lib/python3.10/site-packages/wbuild/wBuild.snakefile", line 10, in
File "/var/folders/7d/rr7nqs8x1wq5rv74p18z5ctr0000gn/T/tmp_w5d0ky_", line 575, in
##############################################################################################

best regards

[ischeller]

Hi @knakamura6222053 ,

it could be that you do not have all the required input files available to run the full pipeline. We had to mask some files before uploading the code as they are not publicly sharable, so it is possible that you won't be able to run the full pipeline for the mitochondrial disease dataset on your side.

If you think you have all the needed input files, you should be able to manually create the file by only running this script. Does this step work for you?

Best,
Ines